메뉴 건너뛰기




Volumn 5, Issue 6, 2010, Pages

Oligonucleotide sequence motifs as nucleosome positioning signals

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; OLIGONUCLEOTIDE;

EID: 77956211432     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010933     Document Type: Article
Times cited : (23)

References (72)
  • 1
    • 0003903126 scopus 로고
    • Springer-Verlag, New York
    • van Holde KE (1989) Chromatin, Springer-Verlag, New York.
    • (1989) Chromatin
    • van Holde, K.E.1
  • 2
    • 0035704707 scopus 로고    scopus 로고
    • Role of DNA sequence in nucleosome stability and dynamics
    • Widom J (2001) Role of DNA sequence in nucleosome stability and dynamics. Q Rev Biophys 34: 269-324.
    • (2001) Q Rev Biophys , vol.34 , pp. 269-324
    • Widom, J.1
  • 3
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: Advances through genomics
    • 10: 161-172
    • Jiang CZ, Pugh BF (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 3: 358-U327.10: 161-172.
    • (2009) Nat Rev Genet , vol.3
    • Jiang, C.Z.1    Pugh, B.F.2
  • 4
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S-cerevisiae
    • Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, et al. (2005) Genome-scale identification of nucleosome positions in S-cerevisiae. Science 309: 626-630.
    • (2005) Science , vol.309 , pp. 626-630
    • Yuan, G.C.1    Liu, Y.J.2    Dion, M.F.3    Slack, M.D.4    Wu, L.F.5
  • 5
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576.
    • (2007) Nature , vol.446 , pp. 572-576
    • Albert, I.1    Mavrich, T.N.2    Tomsho, L.P.3    Qi, J.4    Zanton, S.J.5
  • 6
    • 34748826166 scopus 로고    scopus 로고
    • A high- resolution atlas of nucleosome occupancy in yeast
    • Lee W, Tillo D, Bray N, Morse RH, Davis RW, et al. (2007) A high- resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
    • (2007) Nat Genet , vol.39 , pp. 1235-1244
    • Lee, W.1    Tillo, D.2    Bray, N.3    Morse, R.H.4    Davis, R.W.5
  • 7
    • 33947514987 scopus 로고    scopus 로고
    • Sequence-directed mapping of nucleosome positions
    • Salih F, Salih B, Trifonov EN (2007) Sequence-directed mapping of nucleosome positions. J Biomol Struct Dyn 24: 489-493.
    • (2007) J Biomol Struct Dyn , vol.24 , pp. 489-493
    • Salih, F.1    Salih, B.2    Trifonov, E.N.3
  • 8
    • 46449112319 scopus 로고    scopus 로고
    • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    • Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083.
    • (2008) Genome Res , vol.18 , pp. 1073-1083
    • Mavrich, T.N.1    Ioshikhes, I.P.2    Venters, B.J.3    Jiang, C.4    Tomsho, L.P.5
  • 10
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • Schones DE, Cui KR, Cuddapah S, Roh TY, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
    • (2008) Cell , vol.132 , pp. 887-898
    • Schones, D.E.1    Cui, K.R.2    Cuddapah, S.3    Roh, T.Y.4    Barski, A.5
  • 11
    • 46449103738 scopus 로고    scopus 로고
    • A highresolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
    • Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, et al. (2008) A highresolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051-1063.
    • (2008) Genome Res , vol.18 , pp. 1051-1063
    • Valouev, A.1    Ichikawa, J.2    Tonthat, T.3    Stuart, J.4    Ranade, S.5
  • 13
    • 68249142923 scopus 로고    scopus 로고
    • Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
    • Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, et al. (2009) Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 16: 847-U870.
    • (2009) Nat Struct Mol Biol , vol.16
    • Zhang, Y.1    Moqtaderi, Z.2    Rattner, B.P.3    Euskirchen, G.4    Snyder, M.5
  • 14
    • 74949110964 scopus 로고    scopus 로고
    • Highresolution nucleosome mapping reveals transcription-dependent promoter packaging
    • Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N (2010) Highresolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 20: 90-100.
    • (2010) Genome Res , vol.20 , pp. 90-100
    • Weiner, A.1    Hughes, A.2    Yassour, M.3    Rando, O.J.4    Friedman, N.5
  • 15
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 17
    • 43149114926 scopus 로고    scopus 로고
    • Re-cracking the nucleosome positioning code
    • Article 14
    • Segal MR (2008) Re-cracking the nucleosome positioning code. Stat Appl Genet Mol Biol 7: Article 14.
    • (2008) Stat Appl Genet Mol Biol , vol.7
    • Segal, M.R.1
  • 18
    • 15744397041 scopus 로고    scopus 로고
    • Chromatin remodeling complexes: Strength in diversity, precision through specialization
    • Cairns BR (2005) Chromatin remodeling complexes: strength in diversity, precision through specialization. Curr Opin Genet Dev 15: 185-190.
    • (2005) Curr Opin Genet Dev , vol.15 , pp. 185-190
    • Cairns, B.R.1
  • 19
    • 33847065486 scopus 로고    scopus 로고
    • The epigenomics of cancer
    • Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128: 683-692.
    • (2007) Cell , vol.128 , pp. 683-692
    • Jones, P.A.1    Baylin, S.B.2
  • 20
    • 34547890019 scopus 로고    scopus 로고
    • Functions of site-specific histone acerylation and deacetylation
    • Shahbazian MD, Grunstein M (2007) Functions of site-specific histone acerylation and deacetylation. Annu Rev Biochem 76: 75-100.
    • (2007) Annu Rev Biochem , vol.76 , pp. 75-100
    • Shahbazian, M.D.1    Grunstein, M.2
  • 21
    • 53249133260 scopus 로고    scopus 로고
    • Control of nucleosome positions by DNA sequence and remodeling machines
    • Schnitzler GR (2008) Control of nucleosome positions by DNA sequence and remodeling machines. Cell Biochem Biophys 51: 67-80.
    • (2008) Cell Biochem Biophys , vol.51 , pp. 67-80
    • Schnitzler, G.R.1
  • 22
    • 33745847547 scopus 로고    scopus 로고
    • Antagonistic forces that position nucleosomes in vivo
    • Whitehouse I, Tsukiyama T (2006) Antagonistic forces that position nucleosomes in vivo. Nat Struct Mol Biol 13: 633-640.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 633-640
    • Whitehouse, I.1    Tsukiyama, T.2
  • 23
    • 33749406106 scopus 로고    scopus 로고
    • Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters
    • Hogan GJ, Lee CK, Lieb JD (2006) Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet 2: 1433-1450.
    • (2006) PLoS Genet , vol.2 , pp. 1433-1450
    • Hogan, G.J.1    Lee, C.K.2    Lieb, J.D.3
  • 24
    • 0018372296 scopus 로고
    • Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones
    • Rhodes D (1979) Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. Nucl Acids Res 6: 1805-1816.
    • (1979) Nucl Acids Res , vol.6 , pp. 1805-1816
    • Rhodes, D.1
  • 25
    • 0011031885 scopus 로고
    • Naturally-occurring poly (dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast
    • Struhl K (1985) Naturally-occurring poly (dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci USA 82: 8419-8423.
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 8419-8423
    • Struhl, K.1
  • 26
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:DT) tracts: Major determinants of nucleosome organization
    • Segal E, Widom J (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 27
    • 63449105244 scopus 로고    scopus 로고
    • Intrinsic variability of gene expression encoded in nucleosome positioning sequences
    • Choi JK, Kim YJ (2009) Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet 41: 498-503.
    • (2009) Nat Genet , vol.41 , pp. 498-503
    • Choi, J.K.1    Kim, Y.J.2
  • 28
    • 0001415964 scopus 로고
    • The pitch of chromatin DNA is reflected in its nucleotide-sequence
    • Trifonov EN, Sussman JL (1980) The pitch of chromatin DNA is reflected in its nucleotide-sequence. Proc Natl Acad Sci USA 77: 3816-3820.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 3816-3820
    • Trifonov, E.N.1    Sussman, J.L.2
  • 29
    • 33749153628 scopus 로고    scopus 로고
    • Nucleosome positions predicted through comparative genomics
    • Ioshikhes IP, Albert I, Zanton SJ, Pugh BF (2006) Nucleosome positions predicted through comparative genomics. Nat Genet 38: 1210-1215.
    • (2006) Nat Genet , vol.38 , pp. 1210-1215
    • Ioshikhes, I.P.1    Albert, I.2    Zanton, S.J.3    Pugh, B.F.4
  • 30
    • 45849135627 scopus 로고    scopus 로고
    • Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions
    • Liu HD, Wu JS, Xie JM, Yang XN, Lu ZH, et al. (2008) Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions. Biophys J 94: 4597-4604.
    • (2008) Biophys J , vol.94 , pp. 4597-4604
    • Liu, H.D.1    Wu, J.S.2    Xie, J.M.3    Yang, X.N.4    Lu, Z.H.5
  • 31
    • 0024297584 scopus 로고
    • The terminus of SV40 DNA-replication and transcription contains a sharp sequence-directed curve
    • Hsieh CH, Griffith JD (1988) The terminus of SV40 DNA-replication and transcription contains a sharp sequence-directed curve. Cell 52: 535-544.
    • (1988) Cell , vol.52 , pp. 535-544
    • Hsieh, C.H.1    Griffith, J.D.2
  • 32
    • 0025690307 scopus 로고
    • Attraction, phasing and neighbor effects of histone octamers on curved DNA
    • Costanzo G, Dimauro E, Salina G, Negri R (1990) Attraction, phasing and neighbor effects of histone octamers on curved DNA. J Mol Biol 216: 363-374.
    • (1990) J Mol Biol , vol.216 , pp. 363-374
    • Costanzo, G.1    Dimauro, E.2    Salina, G.3    Negri, R.4
  • 33
    • 0033578872 scopus 로고    scopus 로고
    • Selective nucleosome disruption by drugs that bind in the minor groove of DNA
    • Fitzgerald DJ, Anderson JN (1999) Selective nucleosome disruption by drugs that bind in the minor groove of DNA. J Biol Chem 274: 27128-27138.
    • (1999) J Biol Chem , vol.274 , pp. 27128-27138
    • Fitzgerald, D.J.1    Anderson, J.N.2
  • 34
    • 1042267433 scopus 로고    scopus 로고
    • Dual role of sequence-dependent DNA curvature in nucleosome stability: The critical test of highly bent Crithidia fasciculata DNA tract
    • Scipioni A, Pisano S, Anselmi C, Savino M, De Santis P (2004) Dual role of sequence-dependent DNA curvature in nucleosome stability: the critical test of highly bent Crithidia fasciculata DNA tract. Biophys Chem 107: 7-17.
    • (2004) Biophys Chem , vol.107 , pp. 7-17
    • Scipioni, A.1    Pisano, S.2    Anselmi, C.3    Savino, M.4    de Santis, P.5
  • 35
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191: 659-675.
    • (1986) J Mol Biol , vol.191 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Travers, A.A.3
  • 36
    • 0032760667 scopus 로고    scopus 로고
    • DNA distortion as a factor in nucleosome positioning
    • Fitzgerald DJ, Anderson JN (1999) DNA distortion as a factor in nucleosome positioning. J Mol Biol 293: 477-491.
    • (1999) J Mol Biol , vol.293 , pp. 477-491
    • Fitzgerald, D.J.1    Anderson, J.N.2
  • 37
    • 34447643262 scopus 로고    scopus 로고
    • Nucleosome positioning determinants
    • Fernandez AG, Anderson JN (2007) Nucleosome positioning determinants. JMol Biol 371: 649-668.
    • (2007) JMol Biol , vol.371 , pp. 649-668
    • Fernandez, A.G.1    Anderson, J.N.2
  • 38
    • 34447627286 scopus 로고    scopus 로고
    • DNA structural and sequence determinants for nucleosome positioning
    • Fitzgerald DJ, Anderson JN (1999) DNA structural and sequence determinants for nucleosome positioning. Gene Ther Mol Biol 4: 349-362.
    • (1999) Gene Ther Mol Biol , vol.4 , pp. 349-362
    • Fitzgerald, D.J.1    Anderson, J.N.2
  • 39
    • 0024373679 scopus 로고
    • DNA conformation and protein-binding
    • Travers AA (1989) DNA conformation and protein-binding. Annu Rev Biochem 58: 427-452.
    • (1989) Annu Rev Biochem , vol.58 , pp. 427-452
    • Travers, A.A.1
  • 40
    • 0038226895 scopus 로고    scopus 로고
    • DNA sequence and structure: Direct and indirect recognition in protein-DNA binding
    • Steffen NR, Murphy SD, Tolleri L, Hatfield GW, Lathrop RH (2002) DNA sequence and structure: direct and indirect recognition in protein-DNA binding. Bioinformatics 18 Suppl 1: S22-30.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Steffen, N.R.1    Murphy, S.D.2    Tolleri, L.3    Hatfield, G.W.4    Lathrop, R.H.5
  • 41
    • 60849083224 scopus 로고    scopus 로고
    • Sequence-dependent Nucleosome Positioning
    • Chung HR, Vingron M (2009) Sequence-dependent Nucleosome Positioning. J Mol Biol 386: 1411-1422.
    • (2009) J Mol Biol , vol.386 , pp. 1411-1422
    • Chung, H.R.1    Vingron, M.2
  • 42
    • 0028225644 scopus 로고
    • The crystal-structure of C-C-A-T-T-A-A-T-G-G - implications for bending of B-DNA at T-A steps
    • Goodsell DS, Kaczorgrzeskowiak M, Dickerson RE (1994) The crystal-structure of C-C-A-T-T-A-A-T-G-G - implications for bending of B-DNA at T-A steps. J Mol Biol 239: 79-96.
    • (1994) J Mol Biol , vol.239 , pp. 79-96
    • Goodsell, D.S.1    Kaczorgrzeskowiak, M.2    Dickerson, R.E.3
  • 43
    • 3142518260 scopus 로고    scopus 로고
    • Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps
    • El Hassan MA, Calladine CR (1997) Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil Trans R Soc Lond Ser A-Math Phys Eng Sci 355: 43-100.
    • (1997) Phil Trans R Soc Lond Ser A-Math Phys Eng Sci , vol.355 , pp. 43-100
    • El Hassan, M.A.1    Calladine, C.R.2
  • 44
    • 0034614483 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: Dinucleotide conformational maps
    • Packer MJ, Dauncey MP, Hunter CA (2000) Sequence-dependent DNA structure: Dinucleotide conformational maps. J Mol Biol 295: 71-83.
    • (2000) J Mol Biol , vol.295 , pp. 71-83
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 45
    • 0026059567 scopus 로고
    • Structure of the B-DNA decamer CC- A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-AG- A-T-T-G-G and C-C-A-G-G-C-C-T-G-G
    • Prive GG, Yanagi K, Dickerson RE (1991) Structure of the B-DNA decamer CC- A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-AG- A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J Mol Biol 217: 177-199.
    • (1991) J Mol Biol , vol.217 , pp. 177-199
    • Prive, G.G.1    Yanagi, K.2    Dickerson, R.E.3
  • 46
    • 0029968821 scopus 로고    scopus 로고
    • Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes
    • Urpi L, Tereshko V, Malinina L, HuynhDinh T, Subirana JA (1996) Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes. Nat Struct Biol 3: 325-328.
    • (1996) Nat Struct Biol , vol.3 , pp. 325-328
    • Urpi, L.1    Tereshko, V.2    Malinina, L.3    Huynhdinh, T.4    Subirana, J.A.5
  • 47
    • 0034614487 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: Tetranucleotide conformational maps
    • Packer MJ, Dauncey MP, Hunter CA (2000) Sequence-dependent DNA structure: Tetranucleotide conformational maps. J Mol Biol 295: 85-103.
    • (2000) J Mol Biol , vol.295 , pp. 85-103
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 48
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs R, West SM, Sosinsky A, Liu P, Mann RS, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461: 1248-U1281.
    • (2009) Nature , vol.461
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5
  • 49
    • 0039837085 scopus 로고    scopus 로고
    • Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences
    • Thastrom A, Lowary PT, Widlund HR, Cao H, Kubista M, et al. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J Mol Biol 288: 213-229.
    • (1999) J Mol Biol , vol.288 , pp. 213-229
    • Thastrom, A.1    Lowary, P.T.2    Widlund, H.R.3    Cao, H.4    Kubista, M.5
  • 50
    • 1942489758 scopus 로고    scopus 로고
    • Nucleosomal locations of dominant DNA sequence motifs for histone - DNA interactions and nucleosome positioning
    • Thastrom A, Bingham LM, Widom J (2004) Nucleosomal locations of dominant DNA sequence motifs for histone - DNA interactions and nucleosome positioning. J Mol Biol 338: 695-709.
    • (2004) J Mol Biol , vol.338 , pp. 695-709
    • Thastrom, A.1    Bingham, L.M.2    Widom, J.3
  • 51
    • 0023777538 scopus 로고
    • Statistical Distributions of Nucleosomes - Nonrandom Locations by a Stochastic Mechanism
    • Kornberg RD, Stryer L (1988) Statistical Distributions of Nucleosomes - Nonrandom Locations by a Stochastic Mechanism. Nucl Acids Res 16: 6677-6690.
    • (1988) Nucl Acids Res , vol.16 , pp. 6677-6690
    • Kornberg, R.D.1    Stryer, L.2
  • 54
    • 0032103910 scopus 로고    scopus 로고
    • Unique translational positioning of nucleosomes on synthetic DNAs
    • Fitzgerald DJ, Anderson JN (1998) Unique translational positioning of nucleosomes on synthetic DNAs. Nucl Acids Res 26: 2526-2535.
    • (1998) Nucl Acids Res , vol.26 , pp. 2526-2535
    • Fitzgerald, D.J.1    Anderson, J.N.2
  • 55
    • 0022477409 scopus 로고
    • DNA bending at adenine thymine tracts
    • Koo HS, Wu HM, Crothers DM (1986) DNA bending at adenine thymine tracts. Nature 320: 501-506.
    • (1986) Nature , vol.320 , pp. 501-506
    • Koo, H.S.1    Wu, H.M.2    Crothers, D.M.3
  • 57
    • 57149119464 scopus 로고    scopus 로고
    • Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
    • Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, et al. (2008) Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals. Plos Comput Biol 4: 25.
    • (2008) Plos Comput Biol , vol.4 , pp. 25
    • Field, Y.1    Kaplan, N.2    Fondufe-Mittendorf, Y.3    Moore, I.K.4    Sharon, E.5
  • 58
    • 74949115966 scopus 로고    scopus 로고
    • Chromatin 'programming' by sequence - is there more to the nucleosome code than %GC?
    • Hughes A, Rando OJ (2009) Chromatin 'programming' by sequence - is there more to the nucleosome code than %GC? J Biol 8: 96.
    • (2009) J Biol , vol.8 , pp. 96
    • Hughes, A.1    Rando, O.J.2
  • 59
    • 75149135277 scopus 로고    scopus 로고
    • G plus C content dominates intrinsic nucleosome occupancy
    • Tillo D, Hughes TR (2009) G plus C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10: 13.
    • (2009) BMC Bioinformatics , vol.10 , pp. 13
    • Tillo, D.1    Hughes, T.R.2
  • 61
    • 0042386600 scopus 로고    scopus 로고
    • Sequencedependent DNA structure: A database of octamer structural parameters
    • Gardiner EJ, Hunter CA, Packer MJ, Palmer DS, Willett P (2003) Sequencedependent DNA structure: A database of octamer structural parameters. J Mol Biol 332: 1025-1035.
    • (2003) J Mol Biol , vol.332 , pp. 1025-1035
    • Gardiner, E.J.1    Hunter, C.A.2    Packer, M.J.3    Palmer, D.S.4    Willett, P.5
  • 62
    • 28444490422 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
    • Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, et al. (2005) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J 89: 3721-3740.
    • (2005) Biophys J , vol.89 , pp. 3721-3740
    • Dixit, S.B.1    Beveridge, D.L.2    Case, D.A.3    Cheatham, T.E.4    Giudice, E.5
  • 63
    • 34147191973 scopus 로고    scopus 로고
    • DNA stretching and extreme kinking in the nucleosome core
    • Ong MS, Richmond TJ, Davey CA (2007) DNA stretching and extreme kinking in the nucleosome core. J Mol Biol 368: 1067-1074.
    • (2007) J Mol Biol , vol.368 , pp. 1067-1074
    • Ong, M.S.1    Richmond, T.J.2    Davey, C.A.3
  • 66
    • 0028264042 scopus 로고
    • Human-Immunodeficiency-Virus integrase directs integration to sites of severe DNA distortion within the nucleosome core
    • Pruss D, Bushman FD, Wolffe AP (1994) Human-Immunodeficiency-Virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc Natl Acad Sci USA 91: 5913-5917.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 5913-5917
    • Pruss, D.1    Bushman, F.D.2    Wolffe, A.P.3
  • 68
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423: 145-150.
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 69
    • 34447644439 scopus 로고    scopus 로고
    • A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucleosome positioning
    • Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB (2007) A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucleosome positioning. J Mol Biol 371: 725-738.
    • (2007) J Mol Biol , vol.371 , pp. 725-738
    • Tolstorukov, M.Y.1    Colasanti, A.V.2    McCandlish, D.M.3    Olson, W.K.4    Zhurkin, V.B.5
  • 70
    • 67749086828 scopus 로고    scopus 로고
    • Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence
    • van Vugt JJFA, de Jager M, Murawska M, Brehm A, van Noort J, et al. (2009) Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence. PLoS ONE 4: e6345.
    • (2009) PLoS ONE , vol.4
    • van Vugt, J.J.F.A.1    de Jager, M.2    Murawska, M.3    Brehm, A.4    van Noort, J.5
  • 71
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 72
    • 0025681521 scopus 로고
    • Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA
    • Lowman H, Bina M (1990) Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA. Biopolymers 30: 861-876.
    • (1990) Biopolymers , vol.30 , pp. 861-876
    • Lowman, H.1    Bina, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.